Summary of what happened:
We ran fmriprep and our html files didn’t show results for the functional scans.
Command used (and if a helper script was used, a link to the helper script or the command generated):
Version:
Environment (Docker, Singularity, custom installation):
Data formatted according to a validatable standard? Please provide the output of the validator:
Relevant log outputs (up to 20 lines):
This was the error message that we received:
File: /home/groups/cbohon/EmotEat/analysis/fmriprep/sub-111/log/20230122-053046_03dede47-9805-43e2-95fc-765bb043dc2e/crash-20230122-053253-mstern1-rotime-d79d2186-c818-400b-959b-90978a0d30c1.txt
Working Directory: /scratch/groups/cbohon/work2/fmriprep_22_0_wf/single_subject_111_wf/func_preproc_task_gonogo_run_04_wf/unwarp_wf/rotime
Inputs:
in_file:
metadata: {'AcquisitionMatrixPE': 128, 'AcquisitionNumber': 1, 'AcquisitionTime': '16:19:45.000000', 'BodyPartExamined': 'HEAD', 'CoilString': '8HRBRAIN', 'ConversionSoftware': 'dcm2niix', 'ConversionSoftwareVersion': 'v1.0.20210317', 'DeviceSerialNumber': '0000415723SCHMR2', 'EchoNumber': 1, 'EchoTime': 0.03, 'FlipAngle': 80, 'ImageOrientationPatientDICOM': [0.99993, 0.00043, 0.01148, 0.00089, 0.99344, -0.11438], 'ImageType': ['ORIGINAL', 'PRIMARY', 'OTHER'], 'ImagingFrequency': 127.765, 'InPlanePhaseEncodingDirectionDICOM': 'ROW', 'InstitutionName': 'Stanford Lucas Center', 'MRAcquisitionType': '2D', 'MagneticFieldStrength': 3, 'Manufacturer': 'GE', 'ManufacturersModelName': 'DISCOVERY MR750', 'Modality': 'MR', 'ParallelReductionFactorInPlane': 2, 'PatientPosition': 'HFS', 'PercentPhaseFOV': 100, 'PercentSampling': 100, 'PhaseEncodingDirection': 'i', 'PixelBandwidth': 500, 'ProcedureStepDescription': 'Brain', 'ProtocolName': 'Bohon_EE_10282021', 'ReconMatrixPE': 64, 'RepetitionTime': 2, 'ScanOptions': 'NONE', 'ScanningSequence': 'RM', 'SequenceVariant': 'NONE', 'SeriesDescription': 'go-nogo1_spiral', 'SeriesNumber': 4, 'SliceThickness': 3.5, 'SoftwareVersions': '27\\LX\\MR Software release:DV26.0_R01_1725.a', 'SpacingBetweenSlices': 3.5, 'StationName': 'lc3t3'}
Traceback (most recent call last):
File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
result["result"] = node.run(updatehash=updatehash)
File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
result = self._run_interface(execute=True)
File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
return self._run_command(execute)
File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 771, in _run_command
raise NodeExecutionError(msg)
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node rotime.
Traceback:
Traceback (most recent call last):
File "/opt/conda/lib/python3.9/site-packages/nipype/interfaces/base/core.py", line 398, in run
runtime = self._run_interface(runtime)
File "/opt/conda/lib/python3.9/site-packages/sdcflows/interfaces/epi.py", line 55, in _run_interface
self._results["readout_time"] = get_trt(
File "/opt/conda/lib/python3.9/site-packages/sdcflows/utils/epimanip.py", line 228, in get_trt
raise ValueError("Unknown total-readout time specification")
ValueError: Unknown total-readout time specification